http://www.dspace.cam.ac.uk:80/handle/1810/221769 Fri, 24 May 2013 12:48:19 GMT 2013-05-24T12:48:19Z http://www.dspace.cam.ac.uk:80/handle/1810/244571 Title: The epidemiology of Lagos bat virus and henipaviruses in straw-coloured fruit bats (Eidolon helvum), using population genetics to infer population connectivity Authors: Peel, Alison Jane Abstract: The straw-coloured fruit bat, Eidolon helvum, has been identified as a reservoir for potentially-zoonotic henipaviruses and Lagos bat virus (LBV) in continental Africa. Longitudinal studies at a large urban colony in Accra, Ghana aim to better understand E. helvum and viral ecology, as well as the nature of human-bat interactions. To assess whether the findings from these studies can be extrapolated across the species’ continental range, more information on the movement ecology of the species and connectivity of populations across its range was required. A multifaceted approach, using techniques from the field of genetics, population ecology, and virology, was used to understand the ways in which the structure and dynamics of fruit bat populations across Africa may affect the viral transmission dynamics within them. Given recent difficulties in using electronic positioning systems on E. helvum to track movement, genetic methods were proposed as the most appropriate way to assess connectivity between populations across such a vast range. Henipavirus and LBV serological analyses were undertaken on samples from 12 populations of E. helvum bats across its continental and offshore-island range. A combination of mitochondrial DNA and microsatellite markers were used to describe the genetic metapopulation structure of E. helvum and data were obtained in each location on population sizes, demographic structure, reproductive and migratory seasonality, as well as bat-human interactions. Consistent with expectations for a vagile migratory species, a panmictic continental population structure was detected across its continental range, although the extent of this panmixia was greater than previously detected in any other mammal or bird. Antibodies to henipaviruses and LBV were detected in all continental populations. Isolated island populations in the Gulf of Guinea were genetically distinct from each other and the continental population. Given the isolation of these island fruit bats and the lack of connectivity with other populations, it was expected that populations would be too small to allow persistence of any viruses that cause acute, immunising infections. Contrary to expectations, island individuals displayed evidence for exposure to both viruses. E. helvum is known to roost close in proximity to human populations across continental Africa, and these results could therefore have important public health implications. Further longitudinal studies across multiple locations and information on social structure, daily and seasonal movements are needed to make inferences about virus transmission dynamics and zoonotic risks within the complex population structure. Description: Access to this thesis is restricted until at least May 2015 for publication reasons Mon, 09 Apr 2012 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244571 2012-04-09T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244244 Title: Characterisation and therapeutic modulation of toll-like receptor signalling in response to the intracellular pathogen F. tularensis Authors: Saint, Richard Abstract: The induction of an innate immune response upon infection is dependent on the detection of the invading organism and the generation of a signalling cascade leading to the production of inflammatory mediators. Toll-like receptors are expressed on multiple cell types and induce the activation of a complex network of signalling pathways containing numerous branches with multiple interactions and cross-talk between the different branches. The TLR system is integral to the generation of a protective immune response and as such is an important target for pathogen-associated modulation. Many bacterial and viral pathogens employ strategies for interrupting or modulating TLR signalling to evade the host immune response. The obligate intracellular bacterial pathogen, F. tularensis, successfully invades and replicates within immune and epithelial cells. However, despite significant research the exact mechanisms used by this pathogen to successfully evade the host immune response remain elusive. To establish the exact signalling events that occur within a host upon infection with F. tularensis, the activation of specific signalling proteins was characterised using in vitro and in vivo models. The MAPKs, ERK and p38, were identified as critical in generating the host response. Furthermore, the temporal regulation of these signalling proteins was found to be bi-phasic with an early transient activation of both ERK and p38 followed by a sustained activation of ERK and a suppression of p38 activation at later time points. The role of ERK was investigated further using a specific inhibitor (PD0325901). Although there was no decrease in bacterial burdens in vitro and no increase in survival in mice treated with PD0325901, the inhibition of ERK activation reduced the secretion of TNF and IL-6 and reduced systemic bacterial proliferation in vivo. The induction of immune signalling cascades requires the activation of one or more receptors. The contribution of TLR2, TLR4 and TLR9 to the immune response to F. tularensis infection was examined using KO cell lines and specific antagonists. TLR2 was confirmed as a receptor for F. tularensis and was observed to play a role in the translational regulation of TNF. A role for TLR4 was also identified and further characterisation identified a potential priming relationship with TLR9. Sub-stimulation of 13 TLR4 by LPS enhanced the response induced by a subsequent stimulation of TLR9 by purified F. tularensis DNA. Overall, this study has provided evidence that, during infection, F. tularensis interacts with innate immune signalling pathways. By simultaneously suppressing p38 activation and prolonging ERK activation F. tularensis is able to regulate cytokine secretion and the induction of host-cell death mechanisms. Furthermore, this work has demonstrated that the activation of TLR9 by F. tularensis genomic DNA can be primed by a prior sub-stimulation of TLR4, although more research is required to fully understand the contribution of this interaction to the pathogenesis of F. tularensis. Tue, 08 Jan 2013 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244244 2013-01-08T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/242000 Title: Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development Authors: Renfree, Marilyn B; Papenfuss, Anthony T; Deakin, Janine E; Lindsay, James; Heider, Thomas; Belov, Katherine; Rens, Willem; Waters, Paul D; Pharo, Elizabeth A; Shaw, Geoff; Wong, Emily SW; Lefèvre, Christophe M; Nicholas, Kevin R; Kuroki, Yoko; Wakefield, Matthew J; Zenger, Kyall R; Wang, Chenwei; Ferguson-Smith, Malcolm; Nicholas, Frank W; Hickford, Danielle; Yu, Hongshi; Short, Kirsty R; Siddle, Hannah V; Frankenberg, Stephen R; Chew, Keng Y; Menzies, Brandon R; Stringer, Jessica M; Suzuki, Shunsuke; Hore, Timothy A; Delbridge, Margaret L; Patel, Hardip; Mohammadi, Amir; Schneider, Nanette Y; Hu, Yanqiu; O'Hara, William; Al Nadaf, Shafagh; Wu, Chen; Feng, Zhi-Ping; Cocks, Benjamin G; Wang, Jianghui; Flicek, Paul; Searle, Stephen MJ; Fairley, Susan; Beal, Kathryn; Herrero, Javier; Carone, Dawn M; Suzuki, Yutaka; Sugano, Sumio; Toyoda,Atsushi; Sakaki, Yoshiyuki; Kondo, Shinji; Nishida, Yuichiro; Tatsumoto, Shoji; Mandiou, Ion; Hsu, Arthur; McColl, Kaighin A; Lansdell, Benjamin; Weinstock, George; Kuczek, Elizabeth; McGrath, Annette; Wilson, Peter; Men, Artem; Hazar-Rethinam, Mehlika; Hall, Allison; Davis, John; Wood, David; Williams, Sarah; Sundaravadanam, Yogi; Muzny, Donna M; Jhangiani, Shalini N; Lewis, Lora R; Morgan, Margaret B; Okwuonu, Geoffrey O; Ruiz, San J; Santibanez, Jireh; Nazareth, Lynne; Cree, Andrew; Fowler, Gerald; Kovar, Christie L; Dinh, Huyen H; Joshi, Vandita; Jing, Chyn; Lara, Fremiet; Thornton, Rebecca; Chen, Lei; Deng, Jixin; Liu, Yue; Shen, Joshua Y; Song, Xing-Zhi; Edson, Janette; Troon, Carmen; Thomas, Daniel; Stephens, Amber; Yapa, Lankesha; Levchenko, Tanya; Gibbs, Richard A; Cooper, Desmond W; Speed, Terence P; Fujiyama, Asao; Graves, Jennifer A M; O'Neill, Rachel J; Pask, Andrew J; Forrest, Susan M; Worley, Kim C Abstract: Background. We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. Results. The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. Conclusions. Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution. Fri, 30 Dec 2011 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/242000 2011-12-30T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241599 Title: Evaluation of the role of location and distance in recruitment in respondent-driven sampling Authors: McCreesh, Nicky; Johnston, Lisa G; Copas, Andrew; Sonnenberg, Pam; Seeley, Janet; Hayes, Richard J; Frost, Simon DW; White, Richard G Abstract: Abstract Background Respondent-driven sampling(RDS) is an increasingly widely used variant of a link tracing design for recruiting hidden populations. The role of the spatial distribution of the target population has not been robustly examined for RDS. We examine patterns of recruitment by location, and how they may have biased an RDS study findings. Methods Total-population data were available on a range of characteristics on a population of 2402 male household-heads from an open cohort of 25 villages in rural Uganda. The locations of households were known a-priori. An RDS survey was carried out in this population, employing current RDS methods of sampling and statistical inference. Results There was little heterogeneity in the population by location. Data suggested more distant contacts were less likely to be reported, and therefore recruited, but if reported more distant contacts were as likely as closer contacts to be recruited. There was no evidence that closer proximity to a village meeting place was associated with probability of being recruited, however it was associated with a higher probability of recruiting a larger number of recruits. People living closer to an interview site were more likely to be recruited. Conclusions Household location affected the overall probability of recruitment, and the probability of recruitment by a specific recruiter. Patterns of recruitment do not appear to have greatly biased estimates in this study. The observed patterns could result in bias in more geographically heterogeneous populations. Care is required in RDS studies when choosing the network size question and interview site location(s). Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Mon, 17 Oct 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241599 2011-10-17T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241592 Title: A first-generation integrated tammar wallaby map and its use in creating a tammar wallaby first-generation virtual genome map Authors: Wang, Chenwei; Deakin, Janine E; Rens, Willem; Zenger, Kyall R; Belov, Katherine; Marshall Graves, Jennifer A; Nicholas, Frank W Abstract: Abstract Background The limited (2X) coverage of the tammar wallaby (Macropus eugenii) genome sequence dataset currently presents a challenge for assembly and anchoring onto chromosomes. To provide a framework for this assembly, it would be a great advantage to have a dense map of the tammar wallaby genome. However, only limited mapping data are available for this non-model species, comprising a physical map and a linkage map. Results We combined all available tammar wallaby mapping data to create a tammar wallaby integrated map, using the Location DataBase (LDB) strategy. This first-generation integrated map combines all available information from the second-generation tammar wallaby linkage map with 148 loci, and extensive FISH mapping data for 492 loci, especially for genes likely to be located at the ends of wallaby chromosomes or at evolutionary breakpoints inferred from comparative information. For loci whose positions are only approximately known, their location in the integrated map was refined on the basis of comparative information from opossum (Monodelphis domestica) and human. Interpolation of segments from the opossum and human assemblies into the integrated map enabled the subsequent construction of a tammar wallaby first-generation virtual genome map, which comprises 14336 markers, including 13783 genes recruited from opossum and human assemblies. Both maps are freely available at http://compldb.angis.org.au. Conclusions The first-generation integrated map and the first-generation virtual genome map provide a backbone for the chromosome assembly of the tammar wallaby genome sequence. For example, 78% of the 10257 gene-scaffolds in the Ensembl annotation of the tammar wallaby genome sequence (including 10522 protein-coding genes) can now be given a chromosome location in the tammar wallaby virtual genome map. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 18 Aug 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241592 2011-08-18T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/240640 Title: Social network analysis of behavioural interactions influencing the development of fin damage in Atlantic salmon (Salmo salar) Authors: Cañon Jones, Hernán Alberto Abstract: The development of fin damage in Atlantic salmon parr was investigated using social network analysis of behavioural interactions occurring under different feeding and stocking conditions. Four separate experiments were carried out in which groups of fish were subjected to a long food restriction period (30 days) described in Chapter 2, high (30 kg/m3) or low (8 kg/m3) fish stocking densities (Chapter 3), predictable or unpredictable food delivery regime (Chapter 4) or a short food restriction period (10 days) described in Chapter 5. Dorsal fin damage (erosion, splits and fin index) was significantly higher in groups of fish subjected to food restriction periods (short and long), held at high stocking density (30 kg/m3) or with an unpredictable food delivery regime. No other fins were found to be affected by fin damage irrespective of the treatment. The social networks based on aggressive interactions showed higher centrality, clustering coefficients, in-degree centrality, out-degree centrality and less dense networks in groups subjected to food restriction (short and long), low stocking densities 8 kg/m3), and unpredictable food delivery. The high centralities and clustering coefficients indicated separation of fish within the groups into initiators of aggression and receivers of aggression. This separation of roles was seen only in the food restricted group, high density groups and unpredictable food delivery groups. Initiators had higher out-degree centrality while receivers showed high in-degree centrality. Also, initiators of aggressive interactions had less fin erosion, higher final weights and higher body lengths than receivers of aggression. The severity of fin damage was significantly higher when this role differentiation occurred, and it was highly correlated with fin biting events. Additionally, overall aggression was higher in food restricted groups, low density groups and unpredictable groups. The dynamic analyses of networks over time (Chapter 6) showed that fish classified as initiators of aggression did not change this behaviour after normal/control environmental conditions were restored (i.e. ad libitum food delivery, low stocking density or predictable food delivery). The latter result indicates that individual fish maintained their behaviour irrespective of their social context, which is consistent with the definition of behavioural syndromes, personalities or temperament defined for other non-human animals. Overall these studies demonstrated the importance of using social network analysis to clearly identify and quantify roles that individual fish assume within their network group and through time based on their behavioural interactions leading to dorsal fin damage and differential physical characteristics. The results are potentially applicable within the commercial aquaculture industry as a valuable technique to evaluate and improve the welfare of farmed fish. Mon, 10 Oct 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/240640 2011-10-10T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/240490 Title: Spatial spread of farm animal diseases Authors: Vernon, Matthew Christopher Abstract: Data on cattle movements within the United Kingdom have recently become available. As part of the conditions for lifting an export ban on British beef following the bovine spongiform encephalopathy epidemic, the European Union required that the UK should have "An effective animal identification and movement recording system". The Cattle Tracing System (CTS) was introduced in September 1998, and the scheme was extended to include all cattle by the beginning of 2001. Contact networks have proved valuable in studying the epidemiology of diseases in man, such as human immunodeficiency virus; the availability of CTS cattle movement data has enabled contact network analysis to be applied to diseases of farm livestock. The CTS data may be represented as a large network; cattle holdings are represented as nodes, with a movement of cattle between holdings being an edge. To address concerns about the quality of this cattle movement data, a field study was conducted on Lewis, one of the Western Isles of Scotland. Farmers were recruited with the assistance of the local veterinary surgeon, and asked to record a range of potential risk behaviours relating to the transmission of infectious diseases (moving livestock, sharing pasture, etc.) for a one-month period. For the study area in question, movements of cattle not reported to CTS (especially to or from common grazing land) were a substantial contribution to the contact network during the study period. A wide range of measures of network structure exist, but their relevance to the dynamics of infectious diseases on networks is unclear. To address this, a discrete-time stochastic SIR simulation model of disease on a network was designed and implemented in software. Using this simulation model, a network model with the key structural features of the CTS contact network was constructed, by considering a range of measures of network structure, and testing resulting model networks against CTS-derived networks. The resulting model was shown to predict the dynamics of a simulated disease model on that contact network more closely than existing models of global network structure. Much work on the contact structure of the UK cattle herd has relied on relatively simple static network representations of movement data. By using simulated diseases, the serious shortcomings of static network representations compared to more complex dynamic network representations were demonstrated. A substantial library of software for the generation and analysis of large networks, and the simulation of disease thereupon, has been produced, and has been made generally available. The design and implementation of this software is discussed, including the algorithms and data structures deployed, as well as validation of the software, and its portability to different computing platforms. Thu, 30 Sep 2010 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/240490 2010-09-30T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238240 Title: The in vivoexpression of actin/salt-resistant hyperactive DNase I inhibits the development of anti-ssDNA and anti-histone autoantibodies in a murine model of systemic lupus erythematosus Authors: Manderson, Anthony P; Carlucci, Francesco; Lachmann, Peter J; Lazarus, Robert A; Festenstein, Richard J; Cook, Herbert T; Walport, Mark J; Botto, Marina Abstract: Abstract Systemic lupus erythematosus (SLE) is characterised by the production of autoantibodies against ubiquitous antigens, especially nuclear components. Evidence makes it clear that the development of these autoantibodies is an antigen-driven process and that immune complexes involving DNA-containing antigens play a key role in the disease process. In rodents, DNase I is the major endonuclease present in saliva, urine and plasma, where it catalyses the hydrolysis of DNA, and impaired DNase function has been implicated in the pathogenesis of SLE. In this study we have evaluated the effects of transgenic over-expression of murine DNase I endonucleases in vivo in a mouse model of lupus. We generated transgenic mice having T-cells that express either wild-type DNase I (wt.DNase I) or a mutant DNase I (ash.DNase I), engineered for three new properties – resistance to inhibition by G-actin, resistance to inhibition by physiological saline and hyperactivity compared to wild type. By crossing these transgenic mice with a murine strain that develops SLE we found that, compared to control non-transgenic littermates or wt.DNase I transgenic mice, the ash.DNase I mutant provided significant protection from the development of anti-single-stranded DNA and anti-histone antibodies, but not of renal disease. In summary, this is the first study in vivo to directly test the effects of long-term increased expression of DNase I on the development of SLE. Our results are in line with previous reports on the possible clinical benefits of recombinant DNase I treatment in SLE, and extend them further to the use of engineered DNase I variants with increased activity and resistance to physiological inhibitors. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Sun, 09 Apr 2006 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238240 2006-04-09T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238216 Title: The multiple sex chromosomes of platypus and echidna are not completely identical and several share homology with the avian Z Authors: Rens, Willem; O'Brien, Patricia C M; Grutzner, Frank; Clarke, Oliver; Graphodatskaya, Daria; Tsend-Ayush, Enkhjargal; Trifonov, Vladimir A; Skelton, Helen; Wallis, Mary C; Johnston, Steve; Veyrunes, Frederic; Graves, Jennifer A M; Ferguson-Smith, Malcolm A Abstract: Abstract Background Sex-determining systems have evolved independently in vertebrates. Placental mammals and marsupials have an XY system, birds have a ZW system. Reptiles and amphibians have different systems, including temperature-dependent sex determination, and XY and ZW systems that differ in origin from birds and placental mammals. Monotremes diverged early in mammalian evolution, just after the mammalian clade diverged from the sauropsid clade. Our previous studies showed that male platypus has five X and five Y chromosomes, no SRY, and DMRT1 on an X chromosome. In order to investigate monotreme sex chromosome evolution, we performed a comparative study of platypus and echidna by chromosome painting and comparative gene mapping. Results Chromosome painting reveals a meiotic chain of nine sex chromosomes in the male echidna and establishes their order in the chain. Two of those differ from those in the platypus, three of the platypus sex chromosomes differ from those of the echidna and the order of several chromosomes is rearranged. Comparative gene mapping shows that, in addition to bird autosome regions, regions of bird Z chromosomes are homologous to regions in four platypus X chromosomes, that is, X1, X2, X3, X5, and in chromosome Y1. Conclusion Monotreme sex chromosomes are easiest to explain on the hypothesis that autosomes were added sequentially to the translocation chain, with the final additions after platypus and echidna divergence. Genome sequencing and contig anchoring show no homology yet between platypus and therian Xs; thus, monotremes have a unique XY sex chromosome system that shares some homology with the avian Z. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Fri, 16 Nov 2007 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238216 2007-11-16T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238045 Title: Ultrasonographic evaluation of the supraspinous ligament in a series of ridden and unridden horses and horses with unrelated back pathology Authors: Henson, Frances M D; Lamas, Luis; Knezevic, Sabina; Jeffcott, Leo B Abstract: Abstract Background Injury to the supraspinous ligament (SSL) is reported to cause back pain in the horse. The diagnosis is based on clinical examination and confirmed by ultrasonographic examination. The ultrasonographic appearance of the supraspinous ligament has been well described, but there are few studies that correlate ultrasonographic findings with clinical pain and/or pathology. This preliminary study aims to test the hypothesis that unridden horses (n = 13) have a significantly reduced frequency of occurrence of ultrasonographic changes of the SSL consistent with a diagnosis of desmitis when compared to ridden horses (n = 13) and those with clinical signs of back pain (n = 13). Results The supraspinous ligament of all horses was imaged between T(thoracic)6-T18 and ultrasonographic appearance. There was an average of 2.08 abnormal images per horse from the whole group. The average number of abnormalities in unridden horses was 4.92, in ridden horses 2.92 and in horses with clinical back pain 4.69. No lesions were found between T6 and T10 and 68% of lesions were found between T14 and T17. No significant difference (p < 0.05) was found between the three groups in the number or location of abnormal images. Conclusion The main conclusion was that every horse in this study (n = 39) had at least one site of SSL desmitis (range 2 to 11). It was clear that ultrasonographically diagnosed SSL desmitis cannot be considered as prima facie evidence of clinically significant disease and further evidence is required for a definitive diagnosis. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 01 Mar 2007 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238045 2007-03-01T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238010 Title: Development of a universal measure of quadrupedal forelimb-hindlimb coordination using digital motion capture and computerised analysis Authors: Hamilton, Lindsay; Franklin, Robin J M; Jeffery, Nick D Abstract: Abstract Background Clinical spinal cord injury in domestic dogs provides a model population in which to test the efficacy of putative therapeutic interventions for human spinal cord injury. To achieve this potential a robust method of functional analysis is required so that statistical comparison of numerical data derived from treated and control animals can be achieved. Results In this study we describe the use of digital motion capture equipment combined with mathematical analysis to derive a simple quantitative parameter – 'the mean diagonal coupling interval' – to describe coordination between forelimb and hindlimb movement. In normal dogs this parameter is independent of size, conformation, speed of walking or gait pattern. We show here that mean diagonal coupling interval is highly sensitive to alterations in forelimb-hindlimb coordination in dogs that have suffered spinal cord injury, and can be accurately quantified, but is unaffected by orthopaedic perturbations of gait. Conclusion Mean diagonal coupling interval is an easily derived, highly robust measurement that provides an ideal method to compare the functional effect of therapeutic interventions after spinal cord injury in quadrupeds. Mon, 17 Sep 2007 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238010 2007-09-17T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237998 Title: Chondrocyte outgrowth into a gelatin scaffold in a single impact load model of damage/repair - effect of BMP-2 Authors: Henson, Frances M D; Vincent, Thea A Abstract: Abstract Background Articular cartilage has little capacity for repair in vivo, however, a small number of studies have shown that, in vitro, a damage/repair response can be induced. Recent work by our group has shown that cartilage can respond to single impact load and culture by producing repair cells on the articular surface. The purpose of this study was to identify whether chondrocyte outgrowth into a 3D scaffold could be observed following single impact load and culture. The effect of bone morphogenic-2 (BMP-2) on this process was investigated. Methods Cartilage explants were single impact loaded, placed within a scaffold and cultured for up to 20 days +/- BMP-2. Cell numbers in the scaffold, on and extruding from the articular surface were quantified and the immunohistochemistry used to identify the cellular phenotype. Results Following single impact load and culture, chondrocytes were observed in a 3D gelatin scaffold under all culture conditions. Chondrocytes were also observed on the articular surface of the cartilage and extruding out of the parent cartilage and on to the cartilage surface. BMP-2 was demonstrated to quantitatively inhibit these events. Conclusion These studies demonstrate that articular chondrocytes can be stimulated to migrate out of parent cartilage following single impact load and culture. The addition of BMP-2 to the culture medium quantitatively reduced the repair response. It may be that the inhibitory effect of BMP-2 in this experimental model provides a clue to the apparent inability of articular cartilage to heal itself following damage in vivo. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Wed, 05 Dec 2007 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237998 2007-12-05T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237989 Title: Secreted factors from olfactory mucosa cells expanded as free-floating spheres increase neurogenesis in olfactory bulb neurosphere cultures Authors: Barraud, Perrine; He, Xiao-ling; Caldwell, Maeve; Franklin, Robin J M Abstract: Abstract Background The olfactory epithelium is a neurogenic tissue comprising a population of olfactory receptor neurons that are renewed throughout adulthood by a population of stem and progenitor cells. Because of their relative accessibility compared to intra-cranially located neural stem/progenitor cells, olfactory epithelium stem and progenitor cells make attractive candidates for autologous cell-based therapy. However, olfactory stem and progenitor cells expand very slowly when grown as free-floating spheres (olfactory-spheres) under growth factor stimulation in a neurosphere assay. Results In order to address whether olfactory mucosa cells extrinsically regulate proliferation and/or differentiation of immature neural cells, we cultured neural progenitor cells derived from mouse neonatal olfactory bulb or subventricular zone (SVZ) in the presence of medium conditioned by olfactory mucosa-derived spheres (olfactory-spheres). Our data demonstrated that olfactory mucosa cells produced soluble factors that affect bulbar neural progenitor cell differentiation but not their proliferation when compared to control media. In addition, olfactory mucosa derived soluble factors increased neurogenesis, especially favouring the generation of non-GABAergic neurons. Olfactory mucosa conditioned medium also contained several factors with neurotrophic/neuroprotective properties. Olfactory-sphere conditioned medium did not affect proliferation or differentiation of SVZ-derived neural progenitors. Conclusion These data suggest that the olfactory mucosa does not contain factors that are inhibitory to neural stem/progenitor cell proliferation but does contain factors that steer differentiation toward neuronal phenotypes. Moreover, they suggest that the poor expansion of olfactory-spheres may be in part due to intrinsic properties of the olfactory epithelial stem/progenitor cell population. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Mon, 18 Feb 2008 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237989 2008-02-18T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237981 Title: Construction of networks with intrinsic temporal structure from UK cattle movement data Authors: Heath, M Fred; Vernon, Matthew C; Webb, Cerian R Abstract: Abstract Background The implementation of national systems for recording the movements of cattle between agricultural holdings in the UK has enabled the development and parameterisation of network-based models for disease spread. These data can be used to form a network in which each cattle-holding location is represented by a single node and links between nodes are formed if there is a movement of cattle between them in the time period selected. However, this approach loses information on the time sequence of events thus reducing the accuracy of model predictions. In this paper, we propose an alternative way of structuring the data which retains information on the sequence of events but which still enables analysis of the structure of the network. The fundamental feature of this network is that nodes are not individual cattle-holding locations but are instead direct movements between pairs of locations. Links are made between nodes when the second node is a subsequent movement from the location that received the first movement. Results Two networks are constructed assuming (i) a 7-day and (ii) a 14-day infectious period using British Cattle Movement Service (BCMS) data from 2004 and 2005. During this time period there were 4,183,670 movements that could be derived from the database. In both networks over 98% of the connected nodes formed a single giant weak component. Degree distributions show scale-free behaviour over a limited range only, due to the heterogeneity of locations: farms, markets, shows, abattoirs. Simulation of the spread of disease across the networks demonstrates that this approach to restructuring the data enables efficient comparison of the impact of transmission rates on disease spread. Conclusion The redefinition of what constitutes a node has provided a means to simulate disease spread using all the information available in the BCMS database whilst providing a network that can be described analytically. This will enable the construction of generic networks with similar properties with which to assess the impact of small changes in network structure on disease dynamics. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 20 Mar 2008 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237981 2008-03-20T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237978 Title: Chromhome: A rich internet application for accessing comparative chromosome homology maps Authors: Nagarajan, Sridevi; Rens, Willem; Stalker, James; Cox, Tony; Ferguson-Smith, Malcolm A Abstract: Abstract Background Comparative genomics has become a significant research area in recent years, following the availability of a number of sequenced genomes. The comparison of genomes is of great importance in the analysis of functionally important genome regions. It can also be used to understand the phylogenetic relationships of species and the mechanisms leading to rearrangement of karyotypes during evolution. Many species have been studied at the cytogenetic level by cross species chromosome painting. With the large amount of such information, it has become vital to computerize the data and make them accessible worldwide. Chromhome http://www.chromhome.org is a comprehensive web application that is designed to provide cytogenetic comparisons among species and to fulfil this need. Results The Chromhome application architecture is multi-tiered with an interactive client layer, business logic and database layers. Enterprise java platform with open source framework OpenLaszlo is used to implement the Rich Internet Chromhome Application. Cross species comparative mapping raw data are collected and the processed information is stored into MySQL Chromhome database. Chromhome Release 1.0 contains 109 homology maps from 51 species. The data cover species from 14 orders and 30 families. The homology map displays all the chromosomes of the compared species as one image, making comparisons among species easier. Inferred data also provides maps of homologous regions that could serve as a guideline for researchers involved in phylogenetic or evolution based studies. Conclusion Chromhome provides a useful resource for comparative genomics, holding graphical homology maps of a wide range of species. It brings together cytogenetic data of many genomes under one roof. Inferred painting can often determine the chromosomal homologous regions between two species, if each has been compared with a common third species. Inferred painting greatly reduces the need to map entire genomes and helps focus only on relevant regions of the chromosomes of the species under study. Future releases of Chromhome will accommodate more species and their respective gene and BAC maps, in addition to chromosome painting data. Chromhome application provides a single-page interface (SPI) with desktop style layout, delivering a better and richer user experience. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Wed, 26 Mar 2008 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237978 2008-03-26T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237970 Title: Flying lemurs - the "flying tree shrews"? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade Authors: Nie, Wenhui; Fu, Beiyuan; O'Brien, Patricia C M; Wang, Jinhuan; Su, Weiting; Tanomtong, Alongklod; Volobouev, Vitaly; Ferguson-Smith, Malcolm A; Yang, Fengtang Abstract: Abstract Background Flying lemurs or Colugos (order Dermoptera) represent an ancient mammalian lineage that contains only two extant species. Although molecular evidence strongly supports that the orders Dermoptera, Scandentia, Lagomorpha, Rodentia and Primates form a superordinal clade called Supraprimates (or Euarchontoglires), the phylogenetic placement of Dermoptera within Supraprimates remains ambiguous. Results To search for cytogenetic signatures that could help to clarify the evolutionary affinities within this superordinal group, we have established a genome-wide comparative map between human and the Malayan flying lemur (Galeopterus variegatus) by reciprocal chromosome painting using both human and G. variegatus chromosome-specific probes. The 22 human autosomal paints and the X chromosome paint defined 44 homologous segments in the G. variegatus genome. A putative inversion on GVA 11 was revealed by the hybridization patterns of human chromosome probes 16 and 19. Fifteen associations of human chromosome segments (HSA) were detected in the G. variegatus genome: HSA1/3, 1/10, 2/21, 3/21, 4/8, 4/18, 7/15, 7/16, 7/19, 10/16, 12/22 (twice), 14/15, 16/19 (twice). Reverse painting of G. variegatus chromosome-specific paints onto human chromosomes confirmed the above results, and defined the origin of the homologous human chromosomal segments in these associations. In total, G. variegatus paints revealed 49 homologous chromosomal segments in the HSA genome. Conclusion Comparative analysis of our map with published maps from representative species of other placental orders, including Scandentia, Primates, Lagomorpha and Rodentia, suggests a signature rearrangement (HSA2q/21 association) that links Scandentia and Dermoptera to one sister clade. Our results thus provide new evidence for the hypothesis that Scandentia and Dermoptera have a closer phylogenetic relationship to each other than either of them has to Primates. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Wed, 30 Apr 2008 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237970 2008-04-30T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237915 Title: Expression of genes associated with immunity in the endometrium of cattle with disparate postpartum uterine disease and fertility Authors: Herath, Shan; Lilly, Sonia T; Santos, Natalia R; Gilbert, Robert O; Goetze, Leopold; Bryant, Clare; White, John O; Cronin, James; Sheldon, I Martin Abstract: Abstract Background Contamination of the uterine lumen with bacteria is ubiquitous in cattle after parturition. Some animals develop endometritis and have reduced fertility but others have no uterine disease and readily conceive. The present study tested the hypothesis that postpartum cattle that develop persistent endometritis and infertility are unable to limit the inflammatory response to uterine bacterial infection. Methods Endometrial biopsies were collected several times during the postpartum period from animals that were subsequently infertile with persistent endometritis (n = 4) or had no clinical disease and conceived to first insemination (n = 4). Quantitative PCR was used to determine the expression of candidate genes in the endometrial biopsies, including the Toll-like receptor (TLR 1 to 10) family of innate immune receptors, inflammatory mediators and their cognate receptors. Selected proteins were examined by immunohistochemistry. Results The expression of genes encoding pro-inflammatory mediators such as interleukins (IL1A, IL1B and IL6), and nitric oxide synthase 2 (NOS2) were higher during the first week post partum than subsequently. During the first week post partum, there was higher gene expression in infertile than fertile animals of TLR4, the receptor for bacterial lipopolysaccharide, and the pro-inflammatory cytokines IL1A and IL1B, and their receptor IL1R2. The expression of genes encoding other Toll-like receptors, transforming growth factor beta receptor 1 (TGFBR1) or prostaglandin E2 receptors (PTGER2 and PTGER4) did not differ significantly between the animal groups. Gene expression did not differ significantly between infertile and fertile animals after the first week postpartum. However, there were higher ratios of IL1A or IL1B mRNA to the anti-inflammatory cytokine IL10, during the first week post partum in the infertile than fertile animals, and the protein products of these genes were mainly localised to the epithelium of the endometrium. Conclusion Cattle may maintain fertility by limiting the inflammatory response to postpartum bacterial infection in the endometrium during the first week after parturition. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Thu, 28 May 2009 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237915 2009-05-28T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237850 Title: Evidence for a lineage of virulent bacteriophages that target Campylobacter Authors: Timms, Andrew R; Cambray-Young, Joanna; Scott, Andrew E; Petty, Nicola K; Connerton, Phillippa L; Clarke, Louise; Seeger, Kathy; Quail, Michael A; Cummings, Nicola; Maskell, Duncan; Thomson, Nicholas R; Connerton, Ian F Abstract: Abstract Background Our understanding of the dynamics of genome stability versus gene flux within bacteriophage lineages is limited. Recently, there has been a renewed interest in the use of bacteriophages as 'therapeutic' agents; a prerequisite for their use in such therapies is a thorough understanding of their genetic complement, genome stability and their ecology to avoid the dissemination or mobilisation of phage or bacterial virulence and toxin genes. Campylobacter, a food-borne pathogen, is one of the organisms for which the use of bacteriophage is being considered to reduce human exposure to this organism. Results Sequencing and genome analysis was performed for two Campylobacter bacteriophages. The genomes were extremely similar at the nucleotide level (≥ 96%) with most differences accounted for by novel insertion sequences, DNA methylases and an approximately 10 kb contiguous region of metabolic genes that were dissimilar at the sequence level but similar in gene function between the two phages. Both bacteriophages contained a large number of radical S-adenosylmethionine (SAM) genes, presumably involved in boosting host metabolism during infection, as well as evidence that many genes had been acquired from a wide range of bacterial species. Further bacteriophages, from the UK Campylobacter typing set, were screened for the presence of bacteriophage structural genes, DNA methylases, mobile genetic elements and regulatory genes identified from the genome sequences. The results indicate that many of these bacteriophages are related, with 10 out of 15 showing some relationship to the sequenced genomes. Conclusions Two large virulent Campylobacter bacteriophages were found to show very high levels of sequence conservation despite separation in time and place of isolation. The bacteriophages show adaptations to their host and possess genes that may enhance Campylobacter metabolism, potentially advantaging both the bacteriophage and its host. Genetic conservation has been shown to extend to other Campylobacter bacteriophages, forming a highly conserved lineage of bacteriophages that predate upon campylobacters and indicating that highly adapted bacteriophage genomes can be stable over prolonged periods of time. Mon, 29 Mar 2010 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237850 2010-03-29T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237843 Title: The effect of oxygen tension on calcium homeostasis in bovine articular chondrocytes Authors: White, Rachel; Gibson, John S Abstract: Abstract Background Articular chondrocytes normally experience a lower O2 tension compared to that seen by many other tissues. This level may fall further in joint disease. Ionic homeostasis is essential for chondrocyte function but, at least in the case of H+ ions, it is sensitive to changes in O2 levels. Ca2+ homeostasis is also critical but the effect of changes in O2 tension has not been investigated on this parameter. Here we define the effect of hypoxia on Ca2+ homeostasis in bovine articular chondrocytes. Methods Chondrocytes from articular cartilage slices were isolated enzymatically using collagenase. Cytoplasmic Ca2+ levels ([Ca2+]i) were followed fluorimetrically using Fura-2 to determine the effect of changes in O2 tension. The effects of ion substitution (replacing extracellular Na+ with NMDG+ and chelating Ca2+ with EGTA) were tested. Levels of reactive oxygen species (ROS) and the mitochondrial membrane potential were measured and correlated with [Ca2+]i. Results A reduction in O2 tension from 20% to 1% for 16-18 h caused [Ca2+]i to approximately double, reaching 105 ± 23 nM (p < 0.001). Ion substitutions indicated that Na+/Ca2+ exchange activity was not inhibited at low O2 levels. At 1% O2, ROS levels fell and mitochondria depolarised. Restoring ROS levels (with an oxidant H2O2, a non-specific ROS generator Co2+ or the mitochondrial complex II inhibitor antimycin A) concomitantly reduced [Ca2+]i. Conclusions O2 tension exerts a significant effect on [Ca2+]i. The proposed mechanism involves ROS from mitochondria. Findings emphasise the importance of using realistic O2 tensions when studying the physiology and pathology of articular cartilage and the potential interactions between O2, ROS and Ca2+. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Sun, 25 Apr 2010 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237843 2010-04-25T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/237842 Title: Multiple rearrangements in cryptic species of electric knifefish, Gymnotus carapo (Gymnotidae, Gymnotiformes) revealed by chromosome painting Authors: Nagamachi, Cleusa Y; Pieczarka, Julio C; Milhomem, Susana S R; O'Brien, Patricia C M; de Souza, Augusto C P; Ferguson-Smith, Malcolm A Abstract: Abstract Background Gymnotus (Gymnotidae, Gymnotiformes) is the Neotropical electric fish genus with the largest geographic distribution and the largest number of species, 33 of which have been validated. The diploid number varies from 2n = 39-40 to 2n = 54. Recently we studied the karyotype of morphologically indistinguishable samples from five populations of G. carapo sensu stricto from the Eastern Amazon of Brazil. We found two cytotypes, 2n = 42 (30 M/SM + 12 ST/A) and 2n = 40 (34 M/SM + 6 ST/A) and we concluded that the differences between the two cryptic species are due to pericentric inversions and one tandem fusion. Results In this study we use for the first time, whole chromosome probes prepared by FACS of the Gymnotus carapo sensu strictu species, cytotype with 2n = 42. Using two color hybridizations we were able to distinguish pairs 1, 2, 3, 7, 9, 14, 16, 18, 19, 20 and 21. It was not possible to separate by FACS and distinguish each of the following chromosome pairs even with dual color FISH: {4,8}; {10,11}; {5,6,17}; {12,13,15}. The FISH probes were then used in chromosome painting experiments on metaphases of the 2n = 40 cytotype. While some chromosomes show conserved synteny, others are rearranged in different chromosomes. Eight syntenic associations were found. Conclusions These results show that the karyotype differences between these cryptic species are greater than assumed by classical cytogenetics. These data reinforce the previous supposition that these two cytotypes are different species, despite the absence of morphological differences. Additionally, the homology of repetitive DNA between the two provides evidence of recent speciation. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Mon, 26 Apr 2010 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/237842 2010-04-26T23:00:00Z